Root microbiome

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The root microbiome (also called rhizosphere microbiome) is the dynamic community of microorganisms associated with plant roots.^[1] Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi, and archaea. The microbial communities inside the root and in the rhizosphere are distinct from each other,^[2] and from the microbial communities of bulk soil,^[3] although there is some overlap in species composition.

Different microorganisms, both beneficial and harmful, affect the development and physiology of plants. Beneficial microorganisms include bacteria that fix nitrogen, various microbes that promote plant growth, mycorrhizal fungi, mycoparasitic fungi, protozoa, and certain biocontrol microorganisms.^[1] Pathogenic microorganisms can also include certain bacteria, fungi, and nematodes that can colonize the rhizosphere. Pathogens are able to compete with protective microbes and break through innate plant defense mechanisms.^[1] Some pathogenic bacteria that can be carried over to humans, such as Salmonella, enterohaemorhagic Escherichia coli, Burkholderia cenocepacia, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia, can also be detected in root microbiomes and other plant tissues.^[1]

Root microbiota affect plant host fitness and productivity in a variety of ways. Members of the root microbiome benefit from plant sugars or other carbon rich molecules. Individual members of the root microbiome may behave differently in association with different plant hosts,^[4] or may change the nature of their interaction (along the mutualist-parasite continuum) within a single host as environmental conditions or host health change.^[5]

Despite the potential importance of the root microbiome for plants and ecosystems, our understanding of how root microbial communities are assembled is in its infancy.^[6][7] This is in part because, until recent advances in sequencing technologies, root microbes were difficult to study due to high species diversity, the large number of cryptic species, and the fact that most species have yet to be retrieved in culture.^[8] Evidence suggests both biotic (such as host identity and plant neighbor) and abiotic (such as soil structure and nutrient availability) factors affect community composition.^{[9][10][11][12][13]}